Environmental exposures that cause DNA damage can promote mutagenesis and cell death, and if left unchecked this damage can promote carcinogenesis. Fortunately, cells can respond to DNA damage by regulating gene expression to coordinate proper DNA repair, replication, cell cycle and metabolism. Years of work in S. cerevisiae and humans have demonstrated that ribonucleotide reductase (RNR) activity, and thus regulation of dNTP levels, is a key control point after DNA damage. In our recent paper we have used systems biology and gene targeted approaches to demonstrate that the S. cerevisiae Rnr1 protein, an essential large subunit of the RNR complex, is specifically degraded via autophagy. Protein degradation is a key control mechanism that can regulate biological processes, and an understudied component of the DNA damage response. We have shown that Rnr1 is specifically packaged into an autophagosome and degraded in response to nutrient stress or pharmacological inhibition of target of rapamycin (TOR). We have also demonstrated that defects in autophagy promote increased Rnr1 protein levels and a DNA damage phenotype when TOR is inhibited. Autophagy is usually involved in bulk degradation. Our novel results highlight targeting of a specific DNA damage response protein by autophagy, and they also connect nutrient sensing to optimization of the DNA damage response. Previous studies in humans report that defects in autophagy promote genome instability. Additionally, mTOR inhibition and the induction of autophagy have been linked to p53 and Ataxia-telangiectasia mutated (ATM) signaling after DNA damage. Allelic loss of the human autophagy gene Beclin 1 leads to genome instability, but the mechanism connecting autophagy to genome maintenance is not well understood. Our findings in S. cerevisiae demonstrate that autophagy controls Rnr1 protein levels and we suggest that human cells defective in autophagy have altered levels of DNA damage response proteins. Mis-regulation of DNA damage response proteins would account for the increased genome instability and carcinogenesis observed in autophagy deficient cells. We hypothesize that autophagy can be used to specifically degrade proteins to optimize the DNA damage response. We will perform genetic, biochemical and proteomic based experiments in S. cerevisiae to test our hypothesis and to define the molecular signals that allow autophagy to target specific proteins for degradation.